From the Savings By Design Online Program Handbook on calculation requirements for the whole building approach:
"Whole building analysis requires the use of a program-approved energy design simulation tool. EnergyPro is an example of a CEC approved software that contains a SBD module [1]. The use of other modeling tools may be acceptable at the discretion of the program administrators."
[1] The whole building modeling software preferred by the Savings By Design program is EnergyPro version 7 and later. Version 7 contains a module dedicated to Savings By Design called the “NR SBD Performance” module.
Savings by design incentives are keyed to % better than the Title 24 standard, which means that your software needs to implement a Title 24 baseline ruleset and be approved by the California Energy Commission (CEC) for Title 24 compliance. CBECC-COM, IES Virtual Environment, and EnergyPro are the 2016 Building Energy Efficiency Standards Approved Computer
Compliance Programs for Nonresidential buildings.
CBECC-COM is the performance approach software that implements the Title 24 ruleset to make your baseline building to prescriptive requirements. CBECC-COM is both a ruleset for making models, and uses OpenStudio/EnergyPlus as the backend for simulation. If you make a model in IES, it will export to a CBECC-COM model. I believe EnergyPro is implementing just the ruleset and not creating an OpenStudio/EnergyPlus model, simulating in DOE-2 instead. Another commenter should correct me if I'm wrong on this.
Per your question, why is EnergyPro preferred? It gives out the preferred report format by program reviewers. Many reviewers don't have a background in simulation, so they want software with limited inputs and outputs they can understand and know that the T24 ruleset was implemented correctly. As the program handbook states, you can use other modeling tools and edit schedules outside of CBECC-COM. You'll need some extensive documentation to walk the program administrator through what you did. The hassle of using a non-approved software could easily take more time and money than the marginal difference in design incentive you will get. There are quite a few HVAC systems designs that can't be modeled in EnergyPro, so I frequently claim less SBD savings that what I actually expect per my OpenStudio/EnergyPlus model.
[EDIT] Per this question on the forum "NR SBD Performance" calculation in Energy Pro you can specify schedules in the EnergyPro SBD module.
You can use CBECC-COM for Savings by Design. The only requirement for the program is that your savings numbers need to come from an approved software that uses CBECC-COM, of which IES and EnergyPro are the only ones.
Thanks for the response. This seems to conflict with what I was told by our SBD rep (though it is very possible I was just confused). Also, if this is the case then it seems odd that the EnergyPro SBD module does not use CBECC-Com, instead it relies on the original EnrgyPro DOE2 based back end to calculate the incentive amount. Based on this it seems like the concern is using custom schedules. It is also very possible different utilities have different approaches.
EnergyPro is DOE-2, but makes the inputs with the Title 24 ruleset implemented in CBECC-COM. See answer below.
To answer plainly... preferences by the administrators who have deep root in DOE-2.
Here is a paper describing the key differences between a compliance run and a saving by design run. Seems to be just schedules and non-lighting internal loads (or as they call them confusingly: "artificial loads"). No mention of CBECC-Com (due mostly to the 2014 publication date, I'd imagine), but i think i am going to try to get approval to submit an modified version of the idfs produced by CBECC-Com, I'll try to update this space with the outcome.